BiosynML project: Development of a versatile XML container format and
tools to support bioinformatic analysis workflows in the field of genomics
and secondary metabolite biosynthesis. It also provides a plugin for the
widely used Geneious software to support biosynthetic gene cluster analysis
and to interface with the popular antiSMASH platform. In addition, it serves as
a bridge for gene cluster submissions using the MIBiG community standard.

Download

Note: version 1.5 adds full bi-directional support for submitting jobs to- and retrieving results from antiSMASH version 3 servers.

Quick guide

Some basic use cases for BiosynML are illustrated in the following. This quick guide is also available for download in
pdf format.
For more details and up-to-date information, please visit the project
wiki.

BiosynML plugin installation

Simply drag and drop the .gplugin file (extracted from the downloaded .zip file) into a
Geneious program window, wait for installation to complete, and restart Geneious. You will notice a new symbol
in the Geneious menu icon bar, and an additional "BiosynML" tab appears in the viewer area. This offers a
tabular overview of biosynthetic gene clusters plus a ball-scheme representation of enzymatic domains. Functions to set
a range of meta information on the pathway are available from the sidebar menu. The plugin also extends Geneious
for importing and exporting documents using the xml-based BiosynML file format.

AntiSMASH job submission and retrieving

BiosynML plugin functions can be used to manually add and edit biosynthetic pathway information in
Geneious,
but information-enhanced documents can be created by submitting the sequence of a biosynthetic pathway
(or an entire genome) online to the antiSMASH annotation engine. The plugin will handle job
submission and retrieval of results, using the BiosynML format as a shuttle between the analysis server and the
Geneious client. This works with both the public antiSMASH
webservice or an in-house server you might have setup using the standalone variant of
antiSMASH, starting with antiSMASH version 3.

Biosynthetic pathway curation

The BiosynML plugin facilitates the creation of detailled biosynthetic pathway annotations,
especially for
modular gene clusters responsible for the production of microbial secondary metabolites. Typical tasks include
refining the automatic predictions obtained by antiSMASH, addition of domains and meta data based on manual
analysis, grouping of domains into functional modules and definition of biosynthetic building blocks. These
information are key to establishing the connection between genes and chemical compounds and also a crucial
prerequisite for the design of experiments to investigate the molecular basis for secondary metabolite formation.

Building blocks registry

Assigning biosynthetic building blocks to enzymatic domains that activate small molecules and
incorporate them into complex products is an important analysis step when dealing with secondary metabolite pathways. The
BiosynML plugin assists this analysis by providing a list of previously observed biosynthetic building blocks,
using shortcodes in agreement with other popular databases from the natural products field (such as e.g. Norine).

Biosynthetic domains directory

A number of recurring enzymatic domains are involved in multi-step biosynthetic pathways, each
with a specific role in precursor selection and activation, linkage of building blocks, or their modification, to name
only a few processes. BiosynML uses an online domain directory that supplies the
common "vocabulary" for biosynthetic pathway annotation, also providing basic information about common domains.

Prepare pathways for MIBiG submission

The MIBiG initiative
aims to
establish a
community repository of annotated natural product biosynthetic pathways according to the MIBiG standard ("Minimal
information on biosynthetic gene clusters"). The BiosynML plugin for Geneious helps users to prepare their
curated pathways for submission into the MIBiG database, by pre-filling many fields in the MIBiG form with
the relevant details.

Comparative pathway analysis

(this part under construction; no detailled information available at this time)